Search found 15 matches

by jbhopkins
2020.05.18 21:34
Forum: Mixtures and Flexible Systems
Topic: Bug in EOM Rsigma calculation?
Replies: 1
Views: 61

Re: Bug in EOM Rsigma calculation?

Turns out I can't attach more than 5 files to a post. Here's the rest of the EOM files. The python script is the 'eom_std_check.txt', which I can't attach as .py.
by jbhopkins
2020.05.18 21:32
Forum: Mixtures and Flexible Systems
Topic: Bug in EOM Rsigma calculation?
Replies: 1
Views: 61

Bug in EOM Rsigma calculation?

Hi folks, I'm using EOM from ATSAS 3.0.1, and I think the Rsigma is being calculated incorrect. Either that or I don't understand how the Rsigma calculation is being done (quite possible). I've attached the results of an EOM run on some good quality data (.dat file also attached). Most of the result...
by jbhopkins
2020.04.24 22:52
Forum: ATSAS Package in General
Topic: Missing manual for datmw?
Replies: 1
Views: 105

Missing manual for datmw?

Hi folks, There doesn't seem to be a manual for datmw. It would be nice to have one, both to help me remember it exists, and to easily see what options are available (plus, I'd like the information on how to cite it!). The datmw -h command from the command line actually prints a pretty good descript...
by jbhopkins
2020.01.08 18:38
Forum: Ab Initio Shape Determination
Topic: Error running dammif with 'small' data
Replies: 1
Views: 228

Error running dammif with 'small' data

Hi folks, I'm using DAMMIF from ATSAS 3.0.0 on MacOS 10.14.6. When I try to run dammif on the attached GNOM .out file in fast mode, I get the following error: "error: initial shape dimensions too small, check units" This happens regardless of whether I run it in interactive mode or with command line...
by jbhopkins
2019.11.07 18:21
Forum: Working with Models
Topic: ATSAS 3.0 damaver error
Replies: 2
Views: 622

ATSAS 3.0 damaver error

Hi folks, Congrats on the ATSAS 3.0 release! However, I've been trying to use it on Windows 10 and I can't get damaver to run. I've tried both from the command line and from Primus. If I install ATSAS 3.0 in the default directory (C:/Program Files (x86)/ATSAS 3.0.0) I get this error when I try to ru...
by jbhopkins
2019.04.30 18:37
Forum: Mixtures and Flexible Systems
Topic: Problem with EOM output pdbs
Replies: 2
Views: 4854

Re: Problem with EOM output pdbs

Al, Thanks for the reply. While you're opening bug reports, can you open one for the fact that the distribution outputs don't report the pool average correctly (it's always 0.00, see attached file for details)? For those with a similar problem, I've attached a python script that renumbers the residu...
by jbhopkins
2019.04.29 16:49
Forum: Mixtures and Flexible Systems
Topic: Problem with EOM output pdbs
Replies: 2
Views: 4854

Problem with EOM output pdbs

Hi folks, I'm running EOM on a heterodimer construct connected by a flexible linker. I'm using ATSAS 2.8.4 on MacOS (my local machine). The structure of both domains is known from MX, and was fixed in EOM. The linker and some N and C terminus regions were left flexible. The pool was generated via RA...
by jbhopkins
2017.09.07 15:48
Forum: SAXS & SANS Software
Topic: BioXTAS RAW - analysis of SAXS and SEC-SAXS data
Replies: 0
Views: 13260

BioXTAS RAW - analysis of SAXS and SEC-SAXS data

Hi all, I wanted to quickly promote the BioXTAS RAW software. Here's a little information about the software: BioXTAS RAW is a GUI based, free, open-source Python program for reduction and analysis of small-angle X-ray solution scattering (SAXS) data. The software is designed for biological SAXS dat...
by jbhopkins
2017.02.01 23:15
Forum: Primary Data Processing
Topic: GNOM 5 doesn't recognize .cfg file
Replies: 4
Views: 7191

Re: GNOM 5 doesn't recognize .cfg file

Daniel, I'm sure it was announced, but I can't say that I pay close attention to all of the package announcements. I also have to admit that I didn't test it previously, as I tend to try to stick to release versions (I have enough trouble with bugs in my own software!). Anyways, I'm sure I can make ...
by jbhopkins
2017.02.01 22:37
Forum: Primary Data Processing
Topic: GNOM 5 doesn't recognize .cfg file
Replies: 4
Views: 7191

Re: GNOM 5 doesn't recognize .cfg file

Daniel, Thanks for the response. You're right in that this particular config file doesn't contain anything fancy (it's just lysozyme data), but I've often used the config file as an easy way to automate generation of P(r) functions, either for lots of files with the same settings (varying just Dmax,...
by jbhopkins
2017.02.01 18:28
Forum: Primary Data Processing
Topic: GNOM 5 doesn't recognize .cfg file
Replies: 4
Views: 7191

GNOM 5 doesn't recognize .cfg file

Hi, I recently upgraded to ATSAS 2.8.0 on Windows 7. I'm trying to run GNOM using the standard .cfg file approach (as described in the manual), but it doesn't seem to recognize it. I've put the cfg in the same folder as my data, but when I run gnom from the command line, it fails to recognize it and...
by jbhopkins
2016.06.13 19:50
Forum: ATSAS Package in General
Topic: Still Can't Install on OSX El Capitan version 10.11.4
Replies: 4
Views: 7724

Re: Still Can't Install on OSX El Capitan version 10.11.4

Alternatively, I've found the version built for 10.9 works fine on 10.11 (for me), and doesn't give that error.
by jbhopkins
2016.05.07 17:14
Forum: Ab Initio Shape Determination
Topic: Run DAMMIF multiple times in interactive mode
Replies: 2
Views: 6220

Re: Run DAMMIF multiple times in interactive mode

Just yesterday I publicly released a new version of the BioXTAS RAW program, which allows you to run the expert (interactive) mode of DAMMIF from a GUI, creating as many runs as you want with the same settings. I haven't tested the custom mode thoroughly yet, but if you wanted to give it a shot I'd ...
by jbhopkins
2016.05.07 17:07
Forum: Mixtures and Flexible Systems
Topic: is OS Yosemite version 10.10.5 compatible with ATSAS 2.7.1?
Replies: 2
Views: 1959

Re: is OS Yosemite version 10.10.5 compatible with ATSAS 2.7

I'm successfully using 2.7.1 on 10.10.5. Can you post the commands you are using and the output?
by jbhopkins
2014.10.22 21:38
Forum: Rigid Body Modelling
Topic: SASREFMX Help
Replies: 1
Views: 9476

SASREFMX Help

Hello, I am investing a tetrameric protein complex made of four identical protein subunits. I have obtained a SAXS profile of the full complex, along with high resolution crystallographic data, and know that the symmetry in the crystal is P222, which matches well with what is observed in solution. U...